May 23, 2008

Human population history with a copying model

The movies of the authors' scenario can be found at the bottom of the link. This bit should be emphasized:

One potential avenue for extending the current approach to achieve this goal would be to impute chromosomes from “ancestral populations,” which would both represent populations that existed in the past and also act as efficient donors for the modern haplotypes.

Rather than seeing human variation as a network of gene exchange between the sampled populations, the goal should be to create a rich history of mankind where the named identifiable present-day populations are seen as leaves of a hidden web of interconnections between inferred, but statistically sound past populations, which in turn would be mapped to historical-archaeological entities.

PLoS Genet 4(5): e1000078. doi:10.1371/journal.pgen.1000078

Inferring Human Colonization History Using a Copying Model

Garrett Hellenthal et al.

Abstract

Genome-wide scans of genetic variation can potentially provide detailed information on how modern humans colonized the world but require new methods of analysis. We introduce a statistical approach that uses Single Nucleotide Polymorphism (SNP) data to identify sharing of chromosomal segments between populations and uses the pattern of sharing to reconstruct a detailed colonization scenario. We apply our model to the SNP data for the 53 populations of the Human Genome Diversity Project described in Conrad et al. (Nature Genetics 38,1251-60, 2006). Our results are consistent with the consensus view of a single “Out-of-Africa” bottleneck and serial dilution of diversity during global colonization, including a prominent East Asian bottleneck. They also suggest novel details including: (1) the most northerly East Asian population in the sample (Yakut) has received a significant genetic contribution from the ancestors of the most northerly European one (Orcadian). (2) Native South Americans have received ancestry from a source closely related to modern North-East Asians (Mongolians and Oroquen) that is distinct from the sources for native North Americans, implying multiple waves of migration into the Americas. A detailed depiction of the peopling of the world is available in animated form.

13 comments:

Interesting excersise but the choice of populations seems a little capricious in fact. I specially miss South Asians (what actually explains the relative lack of connection between Western and Eastern Eurasians) and also think that Mozabites look a bad choice for the Africa-Eurasia connection as well (rather a mixed population).

The ignorance of South Asians in any study that attempts to research the spread of humankind out of Africa is not justified in any case, knowing as we do now that this region surely played a major role in the Eurasian dispersal.

It's worth noting Yakuts carry Tat C Y chromosomes at high frequencies. The findings of this team are consistent with the belief that N3 (Tat C) Y chromosomes diffused from Northeastern Europeans to Siberians rather than the reverse.

Yakuts have some European mtDNA which is sufficient to explain their partial European ancestry. Haplogroup N3 is not Western Eurasian, but rather Proto-Uralic, i.e., non-Caucasoid and originated in present-day China. The link provided by n/a quotes Prof. Villems from 2001; however, Villems is the co-author of the 2006 study which ascribes its origin in China.

Much of the reasoning in the "counter-clockwise northern route" paper is awful, but here are some relevant excerpts: Morenotable, however, is the fact that the spatial dynamics ofthe whole N and O haplogroups greatly differ from eachother. The split between N* and O is dated to 34.674.7thousand years (ky). The age of STR variation of hg O inSoutheast Asia probably exceeds 26 ky,10[. . .]In this regard, the age of accumulated STR variation in hgN, estimated on all combined data from N1, N2 and N3 at15 loci (Supplementary Table 2), yields an estimate of19.474.8 ky. However, as will be argued below, theEuropean subcluster of N2 and the Yakutian N3 mighthave descended from single founders with multiple jumpsat several loci, thus causing a possible shift in statisticalestimates that assume a step-wise mutation model. Whenthose chromosomes are excluded, the age of hg N STRdiversity is somewhat younger, 14.274.0 ky.[. . .]NortheasternEurope can be considered as a place of secondaryexpansion of N3. Indeed, hg N3 occurs at high frequenciesin the Volga-Ural Ugric groups and related Finns, Saamiand Estonians. One may notice that while STR variation isrelatively low in the Volga-Ural group, some north-European populations have high STR variance (eg, 0.32 inFinns: data from,36 without DYS385ab).[. . .]Phylogenetic analysis of STR variation (Figure 3) showstwo overlapping subclusters of N3, one of them encompassingpredominantly Volga-Ural region, Finnic- as well asTurkic-speaking populations together with Altaian, and theother one both Baltic-Finnic (Estonians, Karelians andVepsa) and east Slavs (Russians, Ukrainians), as well asWest-Slavonic Slovak N3 chromosomes. The Yakut Ychromosomes form their specific branch; they are almostidentical to each other, consistent with earlier studies.

From an even more recent paper co-authored by Villems:

The presence of hg N (shared by many East Europeanand Northeast Asian populations) in Russians is incontrast with the very limited and spotty presence of othertypically East Asian NRY variants, such as Q and C in theRussian Y chromosomal pool (Table 2). In this sense, ourresults, encompassing the historical Russian area, are ina good agreement with the earlier results on central-southernRussians.14 More generally, it appears that there hasbeen only limited general east-to-west flow of Y chromosomesalongside the steppe belt over long prehistoric andhistoric times, possibly even since the peopling of the temperatezone of Eurasia by anatomically modern humans.That leaves hg N which probably reached East Europealready around the beginning of Holocene the onlyprominent Y chromosomal ‘‘common denominator’’ forthe North-East Asian and East European paternal heritage.

dienekes claims: "Yakuts have some European mtDNA which is sufficient to explain their partial European ancestry."

The Li paper suggests Yakuts are autosomally about 10% European. As far as I know, Yakuts have much less than 20% European mtDNA.

dienekes claims: "Haplogroup N3 is not Western Eurasian, but rather Proto-Uralic,"

The attempt to identify N3 with a supposed skull type makes no sense, of course. N3 originated over 10,000 years ago. We have no idea of the racial type of the individual in whom N3 originated. Moving forward to the present, millions of Caucasoid NE Europeans carry N3, as do some number of Mongoloid and racially-mixed North and East Asians.

Nor does the study dienekes links support his "non-Caucasoid" claim.Even if a distinct "Proto-Uralic" type ancestral to modern Uralics (in varying proportions) existed at one time, the question of where the ancestors of this group came from and which groups they were most closely affiliated with racially would remain. E.g., were they cold-adapted Caucasoids?

The Li paper suggests Yakuts are autosomally about 10% European. As far as I know, Yakuts have much less than 20% European mtDNA.

The Yakuts originated in Lake Baykal, which is the easternmost boundary of Caucasoid expansions according to Russian anthropologists. They could easily have picked up some Caucasoid DNA from there.

Also, both Russians and Finns show admixture with Asian populations, both have very little Asian mtDNA, or Asian Y chromosomes other than N3 (in the case of the Russians, they also have N2, but this is 0-3.3% in the two recent Y chromosome studies in the region of Vologda).

I'd like to see a comparison of the STR diversity between the East Asian subclades of haplogroup N (i.e. N1*-LLY22g(xN1a, N1b, N1c) and N1a) and the Northeast European/Siberian subclades of haplogroup N (i.e. N1b and N1c). This might help to elucidate the region of origin of haplogroup N. In terms of the raw numbers, there should be at least as many haplogroup N individuals in East/Southeast Asia as there are in Europe and Siberia.

We also need to determine more precisely the branching order within haplogroup N, preferably through new SNPs.

N as a whole is clearly Eastern Eurasian. NO* is only found in East Asia and that's also the case of N* (Shanghai, Cambodia). Now N3 may (and probably did) have a more western or at least northern origin. Certainly the main area of distribution of N is Northern Eurasia, rather than its ancestral East Asia, where it's quite rare nowadays.

In any case haplogroups are not races. Just paternal (or maternal in the case of mtDNA) lineages. The overall genetics defining phenotype may perfectly be almost totally unrelated.

"Based on STR variance analysis we observed that hg N3a is more diverse in Eastern Europe than in south Siberia. However, analysis of median networks showed that there are two STR subclusters of hg N3a, N3a1 and N3a2, that are characterized by different genetic histories. Age calculation of STR variation within subcluster N3a1 indicated that its first expansion occurred in south Siberia [approximately 10,000 years (ky)] and then this subcluster spread into Eastern Europe where its age is around 8 ky ago. Meanwhile, younger subcluster N3a2 originated in south Siberia (probably in the Baikal region) approximately 4 ky ago."

"The data obtained allow us to suggest Siberian origin of haplogroups N3 and N2 that are currently widespread in some populations of Eastern Europe."

Xue et al. (2006) found Haplogroup N1*-LLY22g(xN1a-M128, N1b-P43, N1c-TAT) in 11.8% (4/34) of a sample of Hani people, a Tibeto-Burman group living mostly in southwestern China. This is the only case I know of in which proven N1*-LLY22g Y-DNA has been found in more than 10% of a sample.

Hammer et al. (2005) found haplogroup N1-LLY22g(xN1a-M128, N1b-P43, N1c1-M178) in 15.0% (6/40) of a sample of southern Han Chinese and 30.2% (13/43) of a sample of Yi people, another Tibeto-Burman-speaking group from southwestern China. Since N1c-TAT(xN1c1-M178) has been found only in one Mongolian as far as I know, all of the N1(xN1a, N1b, N1c1) Y-DNA found among southern Han Chinese and Yi people is probably actually N1*(xN1a, N1b, N1c), so it looks like the populations that have significant amounts of N1*-LLY22g are Yi people, Hani people (who themselves claim to be derived from Yi people), and Han Chinese (especially those from the southern parts of the country).

However, then another problem arises: Yi and Hani people are supposed to be closely related to one another, and Han Chinese may also share some common ancestry with these Lolo-Burmese ethnic groups, so there is a fairly great probability that the large numbers of N1*-LLY22g Y-chromosomes found in these populations belongs to a single yet-undefined subclade of N1-LLY22g, such as "N1d" or "pre-N1a" or something of that sort.

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